Luo, D., Kato, D., Nogami, J., Ohkawa, Y., Kurumizaka, H., and Kono, H., (2018) MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Nucleic Acids Research. 46: 7124-7137 https://doi.org/10.1093/nar/gky502

Kono, H., Sakuraba, S., and Ishida, H., (2018) Free Energy Profiles for Unwrapping the Outer Superhelical Turn of Nucleosomal DNA. PLoS Comp. Biol. 14: e1006024 https://doi.org/10.1371/journal.pcbi.1006024

池部仁善, 櫻庭俊, and 河野秀俊, (2017) ヌクレオソーム中におけるヒストンテールの特性とアセチル化の影響 (H3 Histone Tail Structure within the Nucleosome and the Impact of the Acetylation). 日本生物物理学会誌. 57: 095-097 https://doi.org/10.2142/biophys.57.095

Tencer, A.H., Cox, K.L., Di, L., Bridgers, J.B., Lyu, J., Wang, X., Sims, J.K., Tyler, Allen, H.F., Zhang, Y., Gatchalian, J., Li, W., Ikebe, J., Wade, P.A., Hayes, J.J., Strahl, B.D., Kono, H., Poirier, M.G., Musselman, C.A., and Kutateladze, T.G., (2017) Covalent modifications of histone H3K9 promote binding of CHD3. Cell Reports. 21: 455-466 https://doi.org/10.1016/j.celrep.2017.09.054

Sunami, T., Chatake, T., and Kono, H., (2017) DNA conformational transitions inferred from reevaluation of m|Fo|-D|Fc| electron density maps. Acta Crystal. D. D73: 600-608 https://doi.org/10.1107/S2059798317007707

Matsumoto, A., Miyazaki, N., Takagi, J., and Iwasaki, K., (2017) 2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching. Scientific Reports. 7: 377 https://doi.org/10.1038/s41598-017-00337-y

Kato, D., Osakabe, A., Mizukami, Y., Adachi, F., Arimura, Y., Saikusa, K., Akashi, S., Nishimura, Y., Park, S.-Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M., and Kurumizaka, H., (2017) Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. Science. 356: 205-208 https://doi.org/10.1126/science.aak9867

Ishida, H. and Kono, H., (2017) H4 tails potentially produce the diversity in the orientation of two nucleosomes. Biophysical J. 113: 978-990 https://doi.org/10.1016/j.bpj.2017.07.015

Gatchalian, J., Wang, X., Ikebe, J., Luo, D., Gibsono, M., Zhang, Y., Cox, K., Musselman, C.A., Poirior, M.G., Kono, H., Haynes, J.J., and Kutateladze, T.G., (2017) Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat. Comm. 8: 1489 https://doi.org/10.1038/s41467-017-01598-x

Andrabi, M., Hutchins, A.P., Miranda-Saavedra, D., Kono, H., Nussinov, R., Mizuguchi, K., and Ahmad, S., (2017) Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Sci Rep. 7: 4071 https://doi.org/10.1038/s41598-017-03199-6

Sakuraba, S. and Kono, H., (2016) Spotting the difference in molecular dynamics simulations of biomolecules. J. Chem. Phys. 145: 074116 https://doi.org/10.1063/1.4961227

Li, Z. and Kono, H., (2016) Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability. Scientific Reports. 6: 31437 https://doi.org/10.1038/srep31437

Ishida, H. and Matsumoto, A., (2016) Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations. Proteins. 84: 1287-1303 https://doi.org/10.1002/prot.25077

Ikebe, J., Sakuraba, S., and Kono, H., (2016) H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. PLoS Comput Biol. 12: e1004788 https://doi.org/10.1371/journal.pcbi.1004788

Kono, H., Shirayama, K., Arimura, Y., Tachiwana, H., and Kurumizaka, H., (2015) Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core. PLoS ONE. 10: e0120635 https://doi.org/10.1371/journal.pone.0120635

Ikebe, J., Umezawa, K., and Higo, J., (2015) Enhanced sampling simulations to construct free-energy landscape of protein?partner substrate interaction. Biophysical Reviews: 1-18 https://doi.org/10.1007/s12551-015-0189-z

櫻庭俊, (2014) 相関から眺める生体分子運動の解析. 統計数理. 62: 171-184

Yang, L., kitano, A., Huang, B., and Go, N., (2014) Ligand-induced protein responses and mechanical signal propagation described by linear response theories. Biophysical Journal 107: 1415-25 https://doi.org/10.1016/j.bpj.2014.07.049

Tsukasaki, Y., Miyazaki, N., Matsumoto, A., Nagae, S., Yonemura, S., Tanoue, T., Iwasaki, K., and Takeichi, M., (2014) Giant cadherins Fat and Dachsous self-bend to organize properly spaced intercellular junctions. Proc Natl Acad Sci U S A. 111: 16011-6 https://doi.org/10.1073/pnas.14189901111418990111 [pii]

Sakuraba, S. and Matsubayashi, N., (2014) ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions. J. Comp. Chem. 35: 1592-608 https://doi.org/10.1002/jcc.23651

Nakagawa, H., Yonetani, Y., Nakajima, K., Ohira-kawamura, S., Kikuchi, T., Inamura, Y., Kataoka, M., and Kono, H., (2014) Local Dynamics Coupled to Hydration Water Determines DNA-sequence Dependent Deformability. Physical Reviews E. 90: 022723-11 https://doi.org/10.1103/PhysRevE.90.022723

Li, H., Sakuraba, S., Chandrasekaran, A., and Yang, L., (2014) Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). Journal of Chemical Information and Modeling. 54: 2275-2285 https://doi.org/10.1021/ci500261z

Kai, T., Tokuhisa, A., Moribayashi, K., Fukuda, Y., Kono, H., and Go, N., (2014) Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses. Journal of the Physical Society of Japan. 83: 094301 https://doi.org/10.7566/JPSJ.83.094301

Ishida, H. and Matsumoto, A., (2014) Free-energy landscape of reverse tRNA translocation through ribosome analyzed by electron microscopy density maps molecular dynamics simulations. PLoS ONE. 9: e101951 https://doi.org/10.1371/journal.pone.0101951

Ishida, H., (2014) Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 82: 1985-1999 https://doi.org/10.1002/prot.24553

Ikebe, J., Sakuraba, S., and Kono, H., (2014) Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules. Journal of Computational Chemistry. 35: 39-50 https://doi.org/10.1002/jcc.23462

池田思朗 and 河野秀俊, (2013) X線自由電子レーザーによる分子の電子密度推定. 統計数理. 61: 135-146

河野秀俊, (2013) 弱い回折パターンからの位相回復：単粒子構造解析に向けて. 日本放射光学会誌「放射光」. 1月号: 38-43

Yonetani, Y. and Kono, H., (2013) Dissociation Free-Energy Profiles of Specific and Nonspecific DNA-Protein Complexes. J Phys Chem B. 117: 7535-45 https://doi.org/10.1021/jp402664w

Tokuhisa, A., Arai, J., Joti, Y., Ohno, Y., Kameyama, T., Yamamoto, K., Hatanaka, M., Gerofi, B., Shimada, A., Kurokawa, M., Shoji, F., Okada, K., Sugimoto, T., Yamaga, M., Tanaka, R., Yokokawa, M., Hori.A., Ishikawa, Y., Hatsui, T., and Go, N., (2013) High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single bio-molecule imaging. Journal of Synchrotron Radiation: 1-16 https://doi.org/10.1107/S0909049513022152

Murakawa, T., Hayashi, H., Sunami, T., Kurihara, K., Tamada, T., Kuroki, R., Suzuki, M., Tanizawa, K., and Okajima, T., (2013) High Resolution Crystal Structure of Copper Amine Oxidase from Arthrobacter globiformis:Identification of Bound O₂-like Diatomic Molecules. Acta Crystallographica Section D, https://doi.org/10.1107/S0907444913023196

Kai, T., Tokuhisa, A., and Kono, H., (2013) Calculation of Molecular-Structure-Based Damage Caused by Short-Pulse High-Intensity X-ray Lasers. Journal of the Physical Society of Japan: 114301-1～5 https://doi.org/10.7566/JPSJ.82.114301 35)

Chatake, T. and Sunami, T., (2013) Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2. Journal of Inorganic Biochemistry. 124: 15-25 https://doi.org/10.1016/j.jinorgbio.2013.03.004 Chatake, T., and Sunami, T. (2013) Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2, Journal of Inorganic Biochemistry 124, 15-25.

Sunami, T. and Kono, H. (2013) Local Conformational Changes in the DNA Interfaces of Proteins. PLoS ONE (Internet), 8, e56080.

Yamasaki, S., Terada, T., Kono, H., Shimizu, K. and Sarai, A. (2012) A New Method for Evaluating the Specificity of Indirect Readout in Protein-DNA Recognition. Nucleic Acids Res., 40, e129.

Adan-Kubo, J., Yoshii, S., Kono, H. and Miyata, M. (2012) Molecular Structure of Isolated MvspI, A Variable Surface Protein of Fish Pathogen Mycoplasma Mobile. J. Bacterio, 194, 3050-3057.

Adan-Kubo, J., Yoshii, S., Kono, H. and Miyata, M. (2012) Molecular Structure of Isolated MvspI, A Variable Surface Protein of Fish Pathogen Mycoplasma Mobile. J. Bacterio, 194, 3050-3057.

Tokuhisa, A., Taka, J., Kono, H. and Go, N. (2012) Classifying and Assembling 2D X-ray Laser Diffraction Patterns of a Single Particle to Reconstruct 3D Diffraction Intensity Function: Resolution Limit Due to The Quantum Noise. Acta Cryst. Sec. A, 68, 366-381.

Yonetani, Y. and Kono, H. (2012) What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences. Biophysical Chemistry, 160, 54-61.

Kono, H., Imanishi, M. et al. (2012) Rational Design of DNA Sequence-Specific Zinc Fingers. FEBS Letters 586: 918-923.

Ikeda, S. and Kono, H. (2012) Phase retrieval from single biomolecule diffraction pattern.Optics Express, 20, 3375-3387.

Ikeda, S. and Kono, H. (2011) Sparse phase retrieval. Proceedings of the Workshop: Signal Processing with Adaptive Sparse Structured Representations (SPARS2011): 106.

Ishida, H. (2011) Molecular Dynamics Simulation System for structural analysis of biomolecules by high performance computing. Progress in Nuclear Science and Technology, 2, 470-476.

Matsumoto, A. (2011) A new approach for building an atomic model from a three-dimensional electron microscopy data. Progress in Nuclear Science and Technology, 2, 486-490.

Higuchi, M., Fujii, J., Yonetani, Y., Kitao, A and Go, N., (2011) Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding. J. Struct. Biol., 173, 20-28.

Ishida, H. (2010) Branch Migration of Holliday Junction in RuvA Tetramer Complex Studied by Umbrella Sampling Simulation Using a Path-search Algorithm. J. Comput. Chem., 31, 2317-2329.

Oikawa, M. and Yonetani, Y. (2010) Molecular Dynamics Free Energy Calculations to Assess the Possibility of Water Existence in Protein Nonpolar Cavities. Biophys. J., 98, 2974-2983.

Matsumoto, A. and Ishida, H. (2009) Global Conformational Changes of Ribosome Observed by Normal Mode Fitting for 3D Cryo-EM Structures. Structure, 17, 1605-1613.

Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. (2009) Discovery of Proteinaceous N-modification in Lysine Biosynthesis of Thermus Thermophilus. Nat. Chem. Biol., 5, 673-679.

Yoshida, A., Tomita, T., Fushinobu, S., Kono, H., Kuzuyama, T. and Makoto, N. (2009) Crystal Structures of the Regulatory Subunit of Thr-sensitive Aspartate Kinase from Themus Thermophilus. FEBS J., 276, 3124-3136.

Yonetani, Y. and Kono, H. (2009) Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove. Biophysical Journal, 97, 1138-1147.

Poornam, G.P., Matsumoto, A., Ishida, H. and Hayward, S. (2009) A Method for the Analysis of Domain Movements in Large Biomolecular Complexes. Proteins, 76, 201-212.

Srinivasan, A.R., Sauers, R.R., Fenley, M.O., Boschitsch, A.H., Matsumoto, A., Colasanti, A.V., and Olson, W. K. (2009) Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA. Biophys. Rev., 1 (1), 13-20.

Ishida, H. and Hayward, S. (2008) Path of Nascent Polypeptide in Exit Tunnel Revealed by Molecular Dynamics Simulation of Ribosome. Biophys. J., 95, 5962-5973.

Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., and Yura, K. (2008) Key interactions in ectodomain of integrin responsible for global conformational change detected by elastic network normal mode analysis. Biophys. J., 95 (6), 2895-2908.

Miyazawa, Y., Nishioka, H., Yura, K., and Yamato, T. (2008) Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. Biophys. J., 94 (6), 2194-2203.

Yonetani, Y., Maruyama, Y., Hirata, F. and Kono, H. (2008) Comparison of DNA Hydration Patterns Obtained Using Two Distinct Computational Methods, Molecular Dynamics Simulation and Three-dimensional Reference Interaction Site Model Theory. J.Chem. Phys., 128, 185102.

Genome Information Integration Project and H-Invitational 2 consortium (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res., 36 D793-D799.

Kono, H., Yuasa, T., Nishiue, S. and Yura, K. (2008) coliSNP Database Server Mapping nsSNPs on Protein Structures. Nucleic Acids Res, 36, D409-D413.

Fujii, S., Kono, H., Takenaka, S., Go, N. and Sarai, A. (2007) Sequence-dependent DNA Deformability Studied using Molecular Dynamics Simulations. Nucleic Acids Res., 35, 6063-6074.

Shiina, J., Oikawa, M., Nakamura, K., Obata, R., and Nishiyama, S. (2007) Synthesis of pingusane-type sesquiterpenoids, acutifolone A and pinguisenol along with bisacutifolones through the Diels-Alder dimerization reaction. Eur. J. Org. Chem., 31 5190-5197.

Yonetani, Y., Kono, H., Fujii, S., Sarai, A. and Go, N. (2007) DNA Deformability and Hydration Studied by Molecular Dynamics Simulation. Mol. Simul., 33, 103-107.

Ishida, H., Kano, T., Yura, K. and Matsumoto, A. (2007) Analysis of Function of a Large-scale Supra-biomolecule System by Molecular Dynamics Simulation System, SCUBA (Simulation Codes for hUge Biomolecular Assembly). Annual Report of the Earth Simulator Center, 257-263.

Tokuhisa, A., Joti, Y., Nakagawa, H., Kitao, A. and Kataoka, M. (2007) Non-Gaussian Behavior of Elastic Inchoherent Neutron Scattering Profile of Protein Studied by Molecular Dynamics Simulation. Physi. Rev. E, 75, 041912.

Gong, X., Nakamura, K., Yu, H., Yura, K., Go, N. (2007) BAAQ: An infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Transactions on Information Technology in Biomedicine, 11 (4), 428-434.

Kawabata, T. and Go, N. (2007) Detection of Pockets on Protein Surfaces Using Small and Large Probe Spheres to Find Putative Ligand Binding Sites. Proteins, 68, 516-529.

Ishida, H., Matsumoto, A., Tsutsumi, Y. and Yura, K. (2006) Conformational Analysis of the Structure of Ribosome Fit into Electron Microscopy Density Maps with Normal Mode Analyses and Molecula Dynamics Simulations. Proceedings of the16th International Microscopy Congress, Proceedings, 242.

Ahmad, S., Kono, H., Arauzo-Bravo, M.J. and Sarai, A. (2006) ReadOut: Structure-based Calculation of Direct and Indirect Readout Energies and Specificities for Protein-DNA Recognition. Nucleic Acids Res., 34, w124-127.

Ishida, H., Higuchi, M., Yonetani, Y., Kano, T., Joti, Y., Kitao, A and Go, N (2006) Analysis of Function of a Large-scale Supra-biomolecule System by Molecular Dynamics Simulation System, SCUBA (Simulation Codes for hUge Biomolecular Assembly). Annual Report of the Earth Simulator Center, 237-240.

Nakagawa, H., Tokuhisa, A., Kamikubo, H., Joti, Y., Kitao, A. and Kataoka, M. (2006) Dynamical Heterogeneity of Protein Dynamics Studied by Elastic Inchoherent Neutron Scattering and Molecular Simulations. Mater. Sci. Eng. A, 422, 356-360.

Nakagawa, H., Kataoka, M., Joti, Y., Kitao, A., Shibata, K., Tokuhisa, A., Tsukushi, I. and Go, N. (2006) Hydration-coupled Protein Boson Peak Measured by Incoherent Neutron Scattering. Physica B-Condensed Matter, 385-86, 871-873.

Yura, K., Yamaguchi, A. and Go, M. (2006) Coverage of whole proteome by structural genomics observed through protein homology modeling database. J. Str. Func. Genomics, 7 (2), 65-76. (Google Scholar Cited by ...)

Kim, O.T., Yura, K. and Go, N. (2006) Amino Acid Residue Doublet Propensity in the Protein-RNA Interface and its Application to RNA Interface Prediction. Nucleic Acids Res., 34, 6450-6460.Google Scholar Cited by ...)

Kitao, A., Yonekura, K., Maki-Yonekura, S., Samatey, F.A., Imada, K., Namba, K. and Go, N. (2006) Switch Interactions Control Energy Frustration and Multiple Flagellar Filament Structures. Proc Natl Acad Sci U.S.A., 103, 4894-4899.

Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T. and Go, M. (2006) Alternative splicing in human transcriptome: functional and structural influence on proteins.Gene, 380 (2), 63-71.(Google Scholar Cited by ...)

Takeda, J., Suzuki, Y., Nakao, M., Barrero, R., Koyanagi, K., Jin, L., Motono, C., Hata, H., Isogai,T., Nagai, K., Otsuki, T., Kuryshev, V., Shionyu, M., Yura, K., Go, M., Thierry-Mieg, J., Thierry-Mieg, D., Wiemann, S., Nomura, N., Sugano, S., Gojobori, T. and Imanishi, T. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res., 34 (14), 3917-3928.(Google Scholar Cited by ...)

Matsumoto, A. and Olson, W. (2006) Predicted Effects of Local Conformational Coupling and External Restraints on the Torsional Properties of Single DNA Molecules. Multiscale Modeling and Simulation,5 (4), 1227-1247.

Mizutani, M.Y., Takamatsu, Y., Ichinose, T., Nakamura, K. and Itai, A., (2006) Effective handling of induced-fit motion in flexible docking. Proteins: Struct. Funct. Bioinf., 63 (4), 878-891.(Google Scholar Cited by ...)

Arauzo-Bravo, M., Fujii, S., Kono, H., Ahmad, S. and Sarai, A. (2005) Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations:Toward Understanding the Indirect Readout Mechanism in Protein-DNA Recognition. J. Am. Chem. Soc., 127, 16074-16089.

Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H. and Sarai, A. (2005) Role of Inter and Intramolecular Interactions in Protein-DNA Recognition. Gene, 364, 108-113.

Nanda, V., Rosenblatt, M.M., Osyczka, A., Kono, H., Getahun, Z., Dutton, P.L., Saven, J.G. and DeGrado, W.F. (2005) De Novo Design of a Redox Active Minimal Rubredoxin Mimic. J. Am. Chem. Soc., 127, 5804 -5805.

Ohgiya, T., Nakamura, K., and Nishiyama, S., (2005)Total Synthesis of (+)-Tanikolide, Using Regioselective Elimination of a Vicinal Dibromoalkane. Bulletin of the Chemical Society of Japan.78, 1549-1554.

Nakamura, K. and Go, N. (2005) Function and molecular evolution of multicopper blue proteins. Cellular and Molecular Life Science 62 (18), 2050-2066.(Google Scholar Cited by ...)

Metsugi, S., Uenoyama, A., Adan, J., Miyata, M., Yura, K., Kono, H. and Go, N. (2005) Sequence Analysis of the Gliding Protein Gli349 in Mycoplasma Mobile. BIOPHYSICS, 1, 33-43.

Metsugi, S. (2005) Influence of Multidimensionality on Convergence of Sampling in Protein Simulation. J. Phys. Soc. Jpn., 74 (6), 1865-1870.

Sarai, A. and Kono, H. (2005) Protein-DNA Recognition Patterns and Predictions. Annu Rev Biophys Biomol Struct., 34, 379-398.

Sarai, A., Siebers, J., Selvaraj, S., Gromiha, M.M. and Kono, H. (2005) Integration of Bioinformatics and Computational Biology to Understand Protein-DNA Recognition Mechanism. J. Bioinform. Comput. Biol., 3, 1-15.

Park, S., Kono, H., Wang, W., Boder, E.T. and Saven, J.G. (2005) Progress in the Development and Application of Computational Methods for Probabilistic Protein Design. Comp. Chem. Eng., 29, 407-421.

Yonetani, Y. (2005) A severe artifact in simulation of liquid water using a long cut-off length: Appearance of a strange layer structure. Chem. Phys. Lett., 406 (1-3), 49-53.(Google Scholar Cited by ...)

Kim, O.T., Yura, K., Go, N. and Harumoto, T. (2005) Newly Sequenced eRF1s from Ciliates: the D versity of Stop Codon Usage and the Molecular Surfaces that are Important for Stop Codon Interactions. Gene, 346, 277-286.

Joti, Y., Kitao, A. and Go, N. (2005) Protein Boson Peak Originated from Hydration-related Multiple Minima Energy Landscape. J Am Chem Soc, 127, 8705-8709.

Kang, A., Kim, S. K., Nakamura, K., Park, J. H., Yoon, Y. J., Lee, K. D., and Yoon, J. (2005) A new cavitand ionophore bearing two rigid crown ether groups. Tetrahedron Lett. 46 (2), 245-248.(Google Scholar Cited by ...)

Gong X.J., Yura, K., and Go, N. (2005) A grid-based system for integrating bioinformatics applications.,Proceedings of the IADIS Applied Computing International Conference 2, 551-558.(Google Scholar Cited by ...)

Matsumoto, A., Tobias, I., and Olson, W.K. (2005) Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 1. Comparison of Computed Motions with the Predicted Behavior of an Ideal Elastic Rod. J. Chem. Theory Comput.1 (1), 117-129.(Google Scholar Cited by ...)

Matsumoto, A., Tobias, I., and Olson, W.K. (2005) Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule. J. Chem. Theory Comput.1 (1), 130-142.(Google Scholar Cited by ...)

Sarai, A., Siebers, J., Selvaraj, S., Gromiha, M. M. and Kono, H. (2004) Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism. Journal of Bioinformatics and Computational Biology 3 (1), 169-183.(Google Scholar Cited by ...)

Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., and Kobayashi, H. (2004)Structure and function of a family 10 beta-xylanase chimera of streptomyces olivaceoviridis E-86 FXYN and cellulomonas fimi Cex. J. Biol. Chem., 279 (25), 26619-26626.(Google Scholar Cited by ...)

Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, T., Tanino, M.,Yura, K., et al. (2004)Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology 2 (6), 0856-0875.(Google Scholar Cited by ...)

Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H. and Sarai, A. (2004) Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition. J. Mol. Biol., 337, 285-294.

Slovic, A.M., Kono, H., Lear, J.D., Saven, J.G. and DeGrado, W.F. (2004) Computational Design of WSK, a Water-Soluble Analogue of the Potassium Channel K sA. Proc. Natl. Acad. Sci. USA, 101, 1828-1833.

Sarai, A., Selvaraj, S., Gromiha, M.M. and Kono, H. (2004) Structure-Function Relationship in DNA Sequence Recognition by Transcription Factors. Aust. Compt. Sci. Comm., 26, 233-238.

Kim, O.T., Yura, K., Go, N. and Harumoto, T. (2004) Highly Divergent Actins from Karyorelictean, Heterotrich, and Litostome Ciliates. J. Eukaryot. Microbiol., 51, 227-233.

Uehara, K., Kawabata, T. and Go, N. (2004) Filtering Remote Homologues Using Predicted Structural Information. Protein Eng., Des. Sel., 17, 565-570.

Basu, G., Sivanesan, D., Kawabata, T. and Go, N. (2004) Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination between Adenine and Guanine-specific Binding Sites. J. Mol. Biol., 342, 1053-1066.

Joti, Y., Kitao, A. and Go, N., (2004) Slow Protein Dynamics to be Detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulation, AIP Conference series, Proceedings of 3rd International Symposium on Slow Dynamics in Complex system, 358-359.

Joti, Y., Kitao, A. and Go, N., (2004) Molecular Simulation Study to Examine the Possibility of Detecting Collective Motion in Protein by Inelastic Neutron Scattering, Physica B, 350, e627-e630 Proceedings of 3rd European Conference on Neutron Scattering,

Nakamura, K., Kawabata, T., Yura, K., and Go, N. (2003) Novel Types of Two-domain Multi-copper Oxidases: Possible Missing Links in the Evolution. FEBS Letters, 553: 239-244.

Matsuda, K., Nishioka, T., Kinoshita,K., Kawabata, T. and Go, N. (2003) Finding Evolutionary Relations Beyond Superfamilies: Fold-based Superfamilies. Protein Sci., 12: 2239-2251.

Yamaguchi, A.,Iida, K., Matsui, N., Tomoda, S., Yura, K., and Go, M. (2004) Het-PDB Navi. : A database for protein-small molecule interactions. J. Biochem. (Tokyo) 135 (1), 79-84.(Google Scholar Cited by ...)

Calhoun, JR., Kono, H., Wang, W., DeGrado, WF., and Saven, JG. (2003) Computational Design and Characterization of a Monomeric Helical Dinuclear Metalloprotein. J. Mol. Biol., 334, 1101-115.

Oobatake, M., Kono, H., Wang, Y. and Sarai, A. (2003) A natomy of Specific Interactions between Lambda Repressor and Operator DNA. Proteins: Struct. Funct. Genet., 53: 33-43.

Fu, X., Kono, H., and Saven, JG. (2003) Probabilistic Approach to the Design of symmetric protein quaternary structures, Protein Eng., 16: 971-977

Yamaguchi, A., Iwadate, M., Suzuki, E., Yura, K., Kawakita, S., Umeyama, H., and Go, M. (2003) Enlarged FAMSBASE: 3D protein structure models of genome sequences for 41 species. Nucleic Acids Res., 31 (1), 463-468.(Google Scholar Cited by ...)

Selvaraj, S., Kono, H., and Sarai, A. (2002) Specificity of Protein-DNA Recognition Revealed by Structure-based Potentials: Asymmetric, Cognate and Non-cognate Binding J. Mol. Biol., 322: 907-915.

Kitao, A. and Takeda, M. (2002) The Effects of Solvent and Anharmonicity on Incoherent Inelastic Neutron Scattering Spectra of Proteins. Journal of Neutron Research, 10: 143-147.

Ishida, H. (2002) Molecular Dynamics Simulation of 7,8-dihydro-8-oxoguanine DNA. J. Biomol. Str. & Dyn., 195: 839-851.

解説

河野秀俊、弱い回折パターンからの位相回復：単粒子構造解析に向けて．日本放射光学会誌「放射光」1月号, pp.38-43.

米谷佳晃、河野秀俊 (2012). 生体分子表面の水分子の滞在時間はどのようにして決まるのか．分子シミュレーション研究会会誌アンサンブル, 14, pp.182-186.

米谷佳晃、河野秀俊 (2010). "DNAの水和水とダイナミクスの塩基配列依存症━DNA－タンパク質、DNA－低分子認識の理解に向けて." メディカルバイオ　揺らぎと生体機能 10月別冊: 66-71.

Kono, H. (2009) Rotamer Libraries for Molecular Modeling and Design of Proteins, "Protein Engineering and Design", (eds Sheldon, P. and Cochran, J.), Taylor and Francis Group, pp. 281-292.

Ishida. H. and Kono, H. (2009) The regulation of the nascent polypeptide in the ribosomal exit tunnel, (ed. R. M. Mohan), RESEARCH ADVANCES IN NUCLEIC ACIDS RESEARCH, (Global Research Network, 2009, Kerala) pp.19-28.

Kinoshita, K., Kono, H. and Yura, Y. (2009) Prediction of Molecular Interactions from 3D-Structures: From Small Ligands to Large Protein Complexes, "Prediction of Protein Structures, Functions, and Interactions", (ed Bujnicki, J.), John Wiley & Sons, pp 159-186.

皿井明倫、河野秀俊. (2007) 蛋白質のDNA認識メカニズムと予測. 生物物理, 47, pp.160-166.

皿井明倫、河野秀俊. (2007) 転写制御における協同性の構造メカニズム. 実験医学増刊　転写因子による生命現象の統合制御 (山本雅之, 五十嵐和彦, 深水昭吉 大熊芳明編). pp.77-84 羊土社

由良敬（分担執筆）. (2007) 「生物物理学ハンドブック」（石渡信一、桂勲、桐野豊、美宅成樹　編集）1.6 ドメイン，モチーフ，モジュール　朝倉書店 pp. 51-53

Go, M., Yura, K. and Shionyu, M. (2007) Contribution of computational biology and structural genomics to understand genome and transcriptome. "Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005)", (eds. Y. Kaneda, H. Kawamura and M. Sasai), Springer, 75-80

Matsumoto, A. and Olson, W.K. (2006) Effects of Sequence, Cyclization, and Superhelical Stress on the Internal Motions of DNA, "Normal Mode Analysis: Theory And Applications to Biological And Chemical Systems (Mathematical and Computational Biology)" (Cui, Q. and Bahar, I. eds.) Crc. Pr. I. Llc. pp. 187-211.

由良敬（分担執筆）. (2006) 「バイオインフォマティクス事典」（日本バイオインフォマティクス学会事典編纂）共立出版 pp.251-258, 601-602, 607-609.

郷信広、米谷佳晃. (2005) 蛋白質がわかるための理論と計算の役割. 生体の科学, 56, pp.626-631.

由良敬、山口晶太、郷通子. (2005) 全ゲノムを対象とした蛋白質立体構造データベースの公開、 蛋白質核酸酵素増刊号「ゲノムから生命システムへ」 共立出版　50 pp. 2301.

由良敬（分担執筆）.(2005) ビタミン、ミネラルのかたち　「食品の科学」（上野川修一、田之倉優　編集）　東京化学同人　２００５年３月刊行.

郷通子、由良敬. (2005) タンパク質のフォールディング 自己組織化と遺伝子のスプライシング　「Bionics」 オーム社　 2, pp. 38-43.

城地保昌、郷信広. (2004) 蛋白質の立体構造ダイナミクスと中性子散乱. 波紋, 14, pp.39-40

由良敬（分担執筆）.(2004) 第６章 データベースの構築と活用　「基礎と演習バイオインフォマティクス」（郷通子、高橋健一編）共立出版 pp.133-164.

Kono, H. and Sarai, A. (2004) Structure-Specificity Relationship in Protein-DNA Recognition, "Bioinformatics of Genome Regulation and Structure" (Kolchanov, N. and Hofestaedt, R. eds.) Kluwer pp. 155-161.

郷信広. (2003) 世界の生物物理学「生物物理学とはなにか」pp.171-179.

由良敬、郷信広. (2003) タンパク質立体構造の進化　「ゲノムからみた生物の多様性と進化」（五條堀孝編集）シュプリンガー・フェアラーク　 pp.33-40.

由良敬. (2003) バイオインフォマティクスが追い求めるもの. 名古屋大学情報連携基盤センターニュース. 2 pp.136-143.

由良敬 (2003) バイオインフォマティクスが追い求めるもの. 名古屋大学情報連携基盤センターニュース. 2 136-143.

河野秀俊、 Saven, J. G. (2003) コンビナトリアルタンパク質設計, 生物物理, 43,pp.186-191.

北尾彰朗. (2002) 分子シミュレーションと中性子散乱による蛋白質のダイナミクス研究. 波紋（日本中性子科学会　学会誌）

北尾彰朗. (2002) 主成分分析を使って眺めた蛋白質のエネルギー地形. ゲノムニュース, 4, pp.61-62

北尾彰朗. (2002) 蛋白質のダイナミクス　化学フロンティア『生体系のコンピュータシミュレーション』（岡本祐幸・岡崎進編）化学同人 pp.140-148

由良敬. (2002) ゲノム配列にもとづくタンパク質機能予測　「プロテオミクスの最新技術」（深見泰夫監修）シーエムシー出版 pp.93-101.

由良敬、郷通子. (2002) モジュールに基づくゲノム機能予測　蛋白質核酸酵素増刊「構造プロテオミクス」 共立出版 47 pp.1090-1096.